Kaiju
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annotation of the assembly with prokka
prokka --locustag SYSA --genus Syngnamydia --species salmonis --strain 4K220114E9 --compliant --centre CHUV Genome_Syngnamydia_4K220114E9.fasta
kaiju
Setup of kaiju database (progenomes)
# Representative genomes from proGenomes makeDB.sh -p
Sompare faa file to kaiju database
kaiju -t ../progenomes/nodes.dmp -f ../progenomes/kaiju_db.fmi -i PROKKA_03062018.faa -p > output.txt
Generate summary file
kaijuReport -i output.txt -o report.tab -t ../progenomes/nodes.dmp -n ../progenomes/names.dmp -r phylum
| % | reads | phylum |
| 44.844597 | 909 | Chlamydiae |
| 7.153429 | 145 | Proteobacteria |
| 3.404046 | 69 | Firmicutes |
| 3.157375 | 64 | Bacteroidetes |
| 1.184016 | 24 | Actinobacteria |
| 0.542674 | 11 | Euryarchaeota |
| 0.444006 | 9 | Cyanobacteria |
| 0.345338 | 7 | Spirochaetes |
| 0.246670 | 5 | Verrucomicrobia |
| 0.246670 | 5 | Candidatus Cloacimonetes |
| 0.197336 | 4 | Deinococcus-Thermus |
| 0.197336 | 4 | Acidobacteria |
| 0.197336 | 4 | Chloroflexi |
| 0.197336 | 4 | Planctomycetes |
| 0.148002 | 3 | Thermodesulfobacteria |
| 0.098668 | 2 | Chlorobi |
| 0.098668 | 2 | Fusobacteria |
| 0.098668 | 2 | Thermotogae |
| 0.098668 | 2 | Balneolaeota |
| 0.049334 | 1 | Candidatus Aminicenantes |
| 0.049334 | 1 | Dictyoglomi |
| 0.049334 | 1 | Gemmatimonadetes |
| 0.049334 | 1 | Aquificae |
| 0.049334 | 1 | Deferribacteres |
| 0.049334 | 1 | Candidatus Poribacteria |
| 0.049334 | 1 | Synergistetes |
| 0.049334 | 1 | Tenericutes |
| 0.049334 | 1 | Thaumarchaeota |
| 0.049334 | 1 | Calditrichaeota |
| 0.000000 | 0 | Viruses |
| 0.789344 | 16 | cannot be assigned to a phylum |
| 35.816479 | 726 | unclassified |
Generate summary file to use for circos
addTaxonNames -t nodes.dmp -n names.dmp -i output.txt -o locus_taxonomy.tab -r phylum
- locus_taxonomy.tab is a two colum file with: locus tag, phylum\_name
- need to be manually edited to add target phylum of interest (max 2, see below)
Self mapping & mummer2circos
Execution (bbmap)
bbmap.sh ref=PROKKA_03022018.fna in1=4K220114E9DNA_CGGAGCCTCCTAGAGT_L002_R1_001_BHB2GGADXX.filt.fastq.gz in2=4K220114E9DNA_CGGAGCCTCCTAGAGT_L002_R2_001_BHB2GGADXX.filt.fastq.gz outm=bbmap_initial.bam
mummer2circos.py -r PROKKA_03022018.fna -q GCF_000237205.1/GCF_000237205.1_ASM23720v1_genomic.fna jellyfish_metagenome/FLZN01000001.fna jellyfish_metagenome/FLZO01000001.fna jellyfish_metagenome/FUHP01000001.fna jellyfish_metagenome/OBEO01000001.fna GCF_000020225.1/GCF_000020225.1_ASM2022v1_genomic.fna GCF_000196115.1/GCF_000196115.1_ASM19611v1_genomic.fna -s PROKKA_03022018.depth -gb PROKKA_03022018.gbf -l -a promer -lt locus_taxonomy.tab
- -lt allow to color CDS based on a taxon table of the followinf format
#Chlamydiae
#Bacteroidetes
SYSA_00001
SYSA_00002 Chlamydiae
SYSA_00003 Chlamydiae
SYSA_00004 Chlamydiae
- the 2 first lines indicates the taxon to color (with #)
- the folowing lines indocates the taxonomy of each locus